We know that Penguin is automated and the unnatural link notifications are manual. So the clear distinction is if you receive a warning in webmaster tools for unnatural links, then it is that. If you saw a drop in rankings when Penguin launched or refreshed then it was Penguin.

But if you didn't have any of those details, how can you tell if a site was hit by Penguin vs unnatural links by just looking at the linkage data?